Sounds like you are missing the footman loop on the inside of the windshield.
It's used to hold the windshield in place when folded down on the hood.
There should be another footman loop lined up in the middle of your hood.
My YJ had the original short strap in place in the footman on the windshield.
I had to remove it when I installed my Bestop Bikini as it utilizes the footman on the windshield, a long strap & buckle from the roll bar to the footman.
I don't what the deal is with the holes in the roll bar.
Maybe a previous owner had speakers up there.